From b655d13069243c5384c194f6bdedb9222d8e649a Mon Sep 17 00:00:00 2001
From: Alexis Thual <alexisthual@gmail.com>
Date: Mon, 12 Feb 2024 12:18:31 +0100
Subject: [PATCH] Allow disabling cache
---
README.md | 3 +-
.../endpoints/alignments_explorer.py | 14 +++-----
.../endpoints/features_explorer.py | 21 +++++++-----
api/src/brain_cockpit/utils.py | 34 ++++++++++++++++---
4 files changed, 50 insertions(+), 22 deletions(-)
diff --git a/README.md b/README.md
index 2839f07..cf4abfe 100644
--- a/README.md
+++ b/README.md
@@ -9,7 +9,8 @@
- large surface fMRI datasets projected on surface meshes
- alignments computed between brains, such as those computed with [fugw](https://alexisthual.github.io/fugw/index.html)
-You can try our [online demo](https://brain-cockpit.athual.fr/)!
+🚀 You can try our [online demo](https://brain-cockpit.tc.humanbrainproject.eu/) displaying the [Individual Brain Charting dataset](https://individual-brain-charting.github.io/docs/), a vast collection of fMRI protocols collected in a small number of human participants.
+This project was deployed with [EBRAINS](https://www.ebrains.eu/).
diff --git a/api/src/brain_cockpit/endpoints/alignments_explorer.py b/api/src/brain_cockpit/endpoints/alignments_explorer.py
index e75aab7..703418d 100644
--- a/api/src/brain_cockpit/endpoints/alignments_explorer.py
+++ b/api/src/brain_cockpit/endpoints/alignments_explorer.py
@@ -1,23 +1,20 @@
+"""Util functions to create Alignments Explorer endpoints."""
+
import os
import pickle
-
from pathlib import Path
import nibabel as nib
import numpy as np
import pandas as pd
+from flask import jsonify, request, send_from_directory
from brain_cockpit.scripts.gifti_to_gltf import create_dataset_glft_files
from brain_cockpit.utils import console, load_dataset_description
-from flask import jsonify, request, send_from_directory
def create_endpoints_one_alignment_dataset(bc, id, dataset):
- """
- For a given alignment dataset, generate endpoints
- serving dataset meshes and alignment transforms.
- """
-
+ """Create all API endpoints for exploring a given Alignments dataset."""
df, dataset_path = load_dataset_description(
config_path=bc.config_path, dataset_path=dataset["path"]
)
@@ -126,8 +123,7 @@ def align_single_voxel():
def create_all_endpoints(bc):
- """Create endpoints for all available alignments datasets."""
-
+ """Create endpoints for all available Alignments datasets."""
if "alignments" in bc.config and "datasets" in bc.config["alignments"]:
# Iterate through each alignment dataset
for dataset_id, dataset in bc.config["alignments"]["datasets"].items():
diff --git a/api/src/brain_cockpit/endpoints/features_explorer.py b/api/src/brain_cockpit/endpoints/features_explorer.py
index dada075..6a45078 100644
--- a/api/src/brain_cockpit/endpoints/features_explorer.py
+++ b/api/src/brain_cockpit/endpoints/features_explorer.py
@@ -1,22 +1,24 @@
+"""Util functions to create Features Explorer endpoints."""
+
import json
import os
-
from pathlib import Path
import nibabel as nib
import numpy as np
import pandas as pd
+from flask import jsonify, request, send_from_directory
from brain_cockpit import utils
from brain_cockpit.scripts.gifti_to_gltf import create_dataset_glft_files
from brain_cockpit.utils import console, load_dataset_description
-from flask import jsonify, request, send_from_directory
# UTIL FUNCTIONS
# These functions are useful for loading data
def hemi_to_side(hemi):
+ """Transform hemisphere label from nilearn to HCP."""
if hemi == "left":
return "lh"
elif hemi == "right":
@@ -25,6 +27,7 @@ def hemi_to_side(hemi):
def side_to_hemi(hemi):
+ """Transform hemisphere label from HCP to nilearn."""
if hemi == "lh":
return "left"
elif hemi == "rh":
@@ -33,6 +36,7 @@ def side_to_hemi(hemi):
def multiindex_to_nested_dict(df):
+ """Transform DataFrame with multiple indices to python dict."""
if isinstance(df.index, pd.core.indexes.multi.MultiIndex):
return dict(
(k, multiindex_to_nested_dict(df.loc[k]))
@@ -46,7 +50,8 @@ def multiindex_to_nested_dict(df):
def parse_metadata(df):
- """
+ """Parse metadata Dataframe.
+
Parameters
----------
df: pandas DataFrame
@@ -84,11 +89,12 @@ def parse_metadata(df):
def create_endpoints_one_features_dataset(bc, id, dataset):
- memory = utils.get_memory(bc)
+ """Create all API endpoints for exploring a given Features dataset."""
- @memory.cache
+ @utils.bc_cache(bc)
def load_data(df, config_path=None, dataset_path=None):
- """
+ """Load data used in endpoints.
+
Parameters
----------
dataset_path: str
@@ -507,8 +513,7 @@ def get_contrast_mean():
def create_all_endpoints(bc):
- """Create endpoints for all available surface datasets."""
-
+ """Create endpoints for all available Features datasets."""
if "features" in bc.config and "datasets" in bc.config["features"]:
# Iterate through each surface dataset
for dataset_id, dataset in bc.config["features"]["datasets"].items():
diff --git a/api/src/brain_cockpit/utils.py b/api/src/brain_cockpit/utils.py
index 08f30e6..c343c13 100644
--- a/api/src/brain_cockpit/utils.py
+++ b/api/src/brain_cockpit/utils.py
@@ -1,10 +1,11 @@
-import os
+"""Util functions used throughout brain-cockpit."""
+import functools
+import os
from pathlib import Path
import pandas as pd
import yaml
-
from joblib import Memory
from rich.console import Console
from rich.progress import (
@@ -24,6 +25,7 @@
# `rich` progress bar used throughout the codebase
def get_progress(**kwargs):
+ """Return rich progress bar."""
return Progress(
SpinnerColumn(),
TaskProgressColumn(),
@@ -38,10 +40,35 @@ def get_progress(**kwargs):
def get_memory(bc):
+ """Return joblib memory."""
return Memory(bc.config["cache_folder"], verbose=0)
+def bc_cache(bc):
+ """Cache functions with brain-cockpit cache."""
+
+ def _inner_decorator(func):
+ @functools.wraps(func)
+ def wrapped(*args, **kwargs):
+ # Use joblib cache if and only if cache_folder is defined
+ if (
+ bc.config["cache_folder"] is not None
+ and bc.config["cache_folder"] != ""
+ ):
+ console.log(f"Using cache {bc.config['cache_folder']}")
+ mem = get_memory(bc)
+ return mem.cache(func)(*args, **kwargs)
+ else:
+ console.log("Not using cache for dataset")
+ return func(*args, **kwargs)
+
+ return wrapped
+
+ return _inner_decorator
+
+
def load_config(config_path=None, verbose=False):
+ """Load brain-cockpit yaml config from path."""
config = None
if config_path is not None and os.path.exists(config_path):
@@ -60,8 +87,7 @@ def load_config(config_path=None, verbose=False):
def load_dataset_description(config_path=None, dataset_path=None):
- """
- Load dataset CSV file.
+ """Load dataset CSV file.
Returns
-------